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1. A chickpea Kunitz trypsin inhibitor is located in cell wall of elongating seedling organs and vascular tissue

Author:
Jiménez, Teresa; Martín, Ignacio; Labrador, Emilia; Dopico, Berta
Source:
Planta 2007 v.226 no.1 pp. 45-55
ISSN:
0032-0935
Subject:
Cicer arietinum; Escherichia coli; Kunitz-type proteinase inhibitor; cell walls; chickpeas; epicotyls; genes; messenger RNA; polyclonal antibodies; seedlings; storage proteins; transcription (genetics); xylem
Abstract:
... Kunitz proteinase inhibitors in legumes have mainly been described as defence and storage proteins. Here, we report a Kunitz trypsin inhibitor, encoded by the CaTPI-1 gene from Cicer arietinum. The transcription of this gene mainly occurs in seedling vegetative organs, and is affected by the light and growth stages. The recombinant TPI-1 protein expressed in E. coli was seen to be an efficient inh ...
DOI:
10.1007/s00425-006-0465-z
PubMed:
17226027

2. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide

Author:
Wadler, Caryn S.; Vanderpool, Carin K.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2007 v.104 no.51 pp. 20454-20459
ISSN:
0027-8424
Subject:
Escherichia coli; alleles; gene expression regulation; glucose; glucose 6-phosphate; glucose transporters; glycolysis; messenger RNA; nucleotides; open reading frames; phenotype; polypeptides; stress response; translation (genetics)
Abstract:
... SgrS is a 227-nt small RNA that is expressed in Escherichia coli during glucose-phosphate stress, a condition associated with intracellular accumulation of glucose-6-phosphate caused by disruption of glycolytic flux. Under stress conditions, SgrS negatively regulates translation and stability of the ptsG mRNA, encoding the major glucose transporter, by means of a base pairing-dependent mechanism r ...
DOI:
10.1073/pnas.0708102104
PubMed:
18042713
PubMed Central:
PMC2154452

3. Anatomy of Escherichia coli σ⁷⁰ promoters

Author:
Shultzaberger, Ryan K.; Chen, Zehua; Lewis, Karen A.; Schneider, Thomas D.
Source:
Nucleic acids research 2007 v.35 no.3 pp. 771-788
ISSN:
0305-1048
Subject:
DNA; Escherichia coli; binding sites; germplasm conservation; mathematical theory; messenger RNA; models; ribosomes; transcription (genetics); transcription factors; translation (genetics); uncertainty
Abstract:
... Information theory was used to build a promoter model that accounts for the -10, the -35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base -7, rather than -11, of the -10 may be flipping to initiate transcription. We found that the sequence conservation of σ⁷⁰ binding sites is 6.5 ± 0.1 bits. Some promoters lack a -35 region, but have a 6.7 ...
DOI:
10.1093/nar/gkl956
PubMed:
17189297
PubMed Central:
PMC1807945

4. A new in vitro translation system for non‐radioactive assay from tobacco chloroplasts: effect of pre‐mRNA processing on translation in vitro

Author:
Yukawa, Maki; Kuroda, Hiroshi; Sugiura, Masahiro
Source:
The plant journal 2007 v.49 no.2 pp. 367-376
ISSN:
0960-7412
Subject:
Escherichia coli; amino acids; chloroplasts; fluorescent dyes; gene expression regulation; green fluorescent protein; messenger RNA; tobacco; transfer RNA
Abstract:
... We previously developed an in vitro translation system derived from tobacco chloroplasts. Here, we report a significantly improved in vitro translation system. By modifying preparation procedures for chloroplast extracts and reaction conditions, we achieved 100‐fold higher translation activity than the previous system. The new system does not require the supplement of Escherichia coli tRNAs due to ...
DOI:
10.1111/j.1365-313X.2006.02948.x

5. AtNUDX1, an 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine 5'-Triphosphate Pyrophosphohydrolase, is Responsible for Eliminating Oxidized Nucleotides in Arabidopsis

Author:
Yoshimura, Kazuya; Ogawa, Takahisa; Ueda, Yayoi; Shigeoka, Shigeru
Source:
Plant & cell physiology 2007 v.48 no.10 pp. 1438-1449
ISSN:
0032-0781
Subject:
risk; green fluorescent protein; DNA damage; Arabidopsis; guanosine; messenger RNA; reactive oxygen species; DNA; nucleotides; cytosol; paraquat; reporter genes; oxidative stress; Escherichia coli
Abstract:
... Cellular DNA, RNA and their precursor nucleotides are at high risk of being oxidized by reactive oxygen species. An oxidized base, 8-oxo-7,8-dihydro-2'-(deoxy)guanosine, can pair with both adenine and cytosine, and thus would cause both replicational and translational errors. Previously, we have reported that an Arabidopsis Nudix hydrolase, AtNUDX1, acts to hydrolyze an oxidized deoxyribonucleotid ...
DOI:
10.1093/pcp/pcm112
PubMed:
17804481

6. Bartonella quintana Lipopolysaccharide Is a Natural Antagonist of Toll-Like Receptor 4

Author:
Popa, Calin; Abdollahi-Roodsaz, Shahla; Joosten, Leo A.B.; Takahashi, Nozomi; Sprong, Tom; Matera, Giovanni; Liberto, Maria Carla; Foca, Alfredo; van Deuren, Marcel; Kullberg, Bart Jan; van den Berg, Wim B.; van der Meer, Jos W.M.; Netea, Mihai G.
Source:
Infection and immunity 2007 v.75 no.10 pp. 4831-4837
ISSN:
0019-9567
Subject:
Bartonella quintana; Escherichia coli; antagonists; bacteremia; fever; gene expression regulation; genes; humans; inflammation; interleukin-1beta; interleukin-6; lipopolysaccharides; messenger RNA; microarray technology; monocytes; tumor necrosis factor-alpha
Abstract:
... Bartonella quintana is a gram-negative microorganism that causes trench fever and chronic bacteremia. B. quintana lipopolysaccharide (LPS) was unable to induce the production of proinflammatory cytokines in human monocytes. Interestingly, B. quintana LPS is a potent antagonist of Toll-like receptor 4 (TLR4), as it inhibited both mRNA transcription and the release of tumor necrosis factor alpha, in ...
DOI:
10.1128/IAI.00237-07
PubMed:
17606598
PubMed Central:
PMC2044526

7. cDNA cloning, expression, protein purification, and characterization of a novel glyoxal oxidase related gene from Vitis pseudoreticulata

Author:
Zhou, B. J.; Wang, X. P.; Wang, Y. J.
Source:
Biologia plantarum 2007 v.51 no.3 pp. 458-466
ISSN:
0006-3134
Subject:
Arabidopsis thaliana; Escherichia coli; Uncinula necator; Vitis; Western blotting; amino acid sequences; amino acids; breeding; complementary DNA; cultivars; disease resistance; gene expression regulation; genes; grapes; inclusion bodies; leaves; messenger RNA; open reading frames; polyclonal antibodies; pressing; rabbits
Abstract:
... To study the defense mechanism of the resistance to the disease of Chinese wild Vitis species and offer powerful bases for the molecular breeding of highly disease-resistant grape cultivars, using mRNA differential display reverse transcript-PCR (DDRT-PCR) and RACE, a full-length cDNA was isolated from Chinese wild Vitis pseudoreticulata clone Baihe-35-1 inoculated with Uncinula necator by pressin ...
DOI:
10.1007/s10535-007-0096-7

8. Characterization of enzymes involved in the ethanol production of Moorella sp. HUC22-1

Author:
Inokuma, Kentaro; Nakashimada, Yutaka; Akahoshi, Takuya; Nishio, Naomichi
Source:
Archives of microbiology 2007 v.188 no.1 pp. 37-45
ISSN:
0302-8933
Subject:
Escherichia coli; Moorella; NAD (coenzyme); NADP (coenzyme); acetaldehyde dehydrogenase; acetates; acetyl coenzyme A; alcohol dehydrogenase; enzyme activity; ethanol; ethanol production; fructose; genes; messenger RNA; oxidation; pH; thermophilic bacteria
Abstract:
... Since the thermophilic bacterium Moorella sp. HUC22-1 produces 120 mM acetate and 5.2 mM ethanol from H₂-CO₂, several candidate genes, which were predicted to code for three alcohol dehydrogenases (AdhA, B, C) and one acetaldehyde dehydrogenase (Aldh), were cloned from HUC22-1. The cloned genes were subcloned into a His-tagged expression vector and expressed in Escherichia coli. Recombinant AdhA a ...
DOI:
10.1007/s00203-007-0221-1
PubMed:
17318639

9. Characterization of the putative iron sulfur protein IdiC (ORF5) in Synechococcus elongatus PCC 7942

Author:
Pietsch, Daniel; Staiger, Dorothee; Pistorius, Elfriede K.; Michel, Klaus-Peter
Source:
Photosynthesis research 2007 v.94 no.1 pp. 91-108
ISSN:
0166-8595
Subject:
transcription factors; messenger RNA; sulfur; viability; starvation; Synechococcus sp. PCC 7942; electron transfer; operon; mutants; photosystem I; chlorophyll; oxygen; ferredoxin-NADP reductase; Escherichia coli
Abstract:
... The IdiC protein (iron deficiency induced protein C) is encoded by orf5 (now called idiC), which is part of the iron-responsive idiB operon of Synechococcus elongatus PCC 7942. The 20.5 kDa IdiC protein has a putative transmembrane helix and belongs to the thioredoxin (TRX)-like [2Fe-2S] ferredoxin family. IdiC has the highest similarity to the peripheral subunit NuoE of the Escherichia coli NDH-1 ...
DOI:
10.1007/s11120-007-9222-9
PubMed:
17690995

10. Chinese herb Radix Polygoni Multiflori as a therapeutic drug for liver cirrhosis in mice

Author:
Huang, C.H.; Horng, L.Y.; Chen, C.F.; Wu, R.T.
Source:
Journal of ethnopharmacology 2007 v.114 no.2 pp. 199-206
ISSN:
0378-8741
Subject:
Oriental traditional medicine; liver cirrhosis; medicinal plants; mice; medicinal properties; plant extracts; coculture; cell proliferation; animal disease models; Escherichia coli; Kupffer cells; dosage; messenger RNA; hepatocyte growth factor; mortality; China
DOI:
10.1016/j.jep.2007.07.034

11. Cloning and functional expression of the mitochondrial alternative oxidase of Aspergillus fumigatus and its induction by oxidative stress

Author:
Magnani, T.; Soriani, F.M.; Martins, V.P.; Nascimento, A.M.; Tudella, V.G.; Curti, C.; Uyemura, S.A.
Source:
FEMS microbiology letters 2007 v.271 no.2 pp. 230-238
ISSN:
0378-1097
Subject:
Aspergillus fumigatus; Escherichia coli; Saccharomyces cerevisiae; electron transport chain; gene expression; genes; heterologous gene expression; menadione; messenger RNA; open reading frames; oxidative stress; oxygen; oxygen consumption; paraquat; potassium cyanide; reactive oxygen species
Abstract:
... Aspergillus fumigatus possesses a branched mitochondrial electron transport chain, with both cyanide-sensitive and -insensitive oxygen-consumption activities. Mitochondrial reactive oxygen species mediate signaling for alternative oxidase (AOX) expression. A 1173 bp-long Afaox gene encoding a 40 kDa protein has been cloned and identified. Recombinant constructs containing the Afaox ORF were transf ...
DOI:
10.1111/j.1574-6968.2007.00716.x
PubMed:
17425662

12. Cloning of metallothionein genes from Arachis hypogaea and characterization of AhMT2a

Author:
Quan, X. Q.; Shan, L.; Bi, Y. P.
Source:
Russian journal of plant physiology 2007 v.54 no.5 pp. 669-675
ISSN:
1021-4437
Subject:
Arachis hypogaea; Escherichia coli; Northern blotting; abscisic acid; amino acids; bacteria; cadmium; complementary DNA; copper; gene expression regulation; genes; heat; heavy metals; hydrogen peroxide; lead; leaves; messenger RNA; metallothionein; nucleotide sequences; peanuts; recombinant proteins; roots; stems
Abstract:
... Seven cDNA sequences putatively encoding metallothionein (MT) proteins were isolated from peanut (Arachis hypogaea L.). We analyzed the sequences of the deduced amino acids and characterized one of these genes, AhMT2a. Northern blot analysis indicates that the accumulation of AhMT2a mRNA was found in stems, young roots, and young leaves, and AhMT2a mRNA levels were up-regulated by cadmium, copper, ...
DOI:
10.1134/S1021443707050159

13. Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting

Author:
Hansen, Thomas M.; Reihani, S. Nader S.; Oddershede, Lene B.; Sørensen, Michael A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2007 v.104 no.14 pp. 5830-5835
ISSN:
0027-8424
Subject:
Escherichia coli; Human immunodeficiency virus; Infectious bronchitis virus; cryo-electron microscopy; deformation; energy; messenger RNA; models; nucleotide sequences; optical traps; pathogens; ribosomes; strength (mechanics); transfer RNA
Abstract:
... Programmed ribosomal frameshifting is often used by viral pathogens including HIV. Slippery sequences present in some mRNAs cause the ribosome to shift reading frame. The resulting protein is thus encoded by one reading frame upstream from the slippery sequence and by another reading frame downstream from the slippery sequence. Although the mechanism is not well understood, frameshifting is known ...
DOI:
10.1073/pnas.0608668104
PubMed:
17389398
PubMed Central:
PMC1838403

14. CpG-ODN enhances mammary gland defense during mastitis induced by Escherichia coli infection in goats

Author:
Zhu, Y.M.; Miao, J.F.; Zhang, Y.S.; Li, Z.; Zou, S.X.; Deng, Y.E.
Source:
Veterinary immunology and immunopathology 2007 v.120 no.3-4 pp. 168-176
ISSN:
0165-2427
Subject:
oligonucleotides; mastitis; messenger RNA; anti-inflammatory activity; bacterial colonization; disease prevention; goats; lactation; dosage; goat milk; injection; immunostimulants; immunization; mammary glands; immune response; goat diseases; Escherichia infections; Escherichia coli
Abstract:
... Seven healthy native goats in early lactation, weighing 30-40 kg, were used in this study. The right mammary gland of the seven does were infused with CpG-ODN at a dosage of 100 μg kg-1 body weight on the day 5 postpartum (PP). The left glands were used as controls and infused with sterile phosphate-buffered saline (PBS). On day 8 PP, the same dosage of CpG-ODN or PBS was again infused. On day 9 P ...
DOI:
10.1016/j.vetimm.2007.08.003

15. Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria

Author:
Horie, Yoshinao; Ito, Yoko; Ono, Miyuki; Moriwaki, Naoko; Kato, Hideki; Hamakubo, Yuriko; Amano, Tomoki; Wachi, Masaaki; Shirai, Makoto; Asayama, Munehiko
Source:
Molecular genetics and genomics 2007 v.278 no.3 pp. 331-346
ISSN:
1617-4615
Subject:
Escherichia coli; Synechocystis; gene expression; genes; messenger RNA; mutants; mutation; nucleotides; ribonucleases
Abstract:
... Light-responsive gene expression is crucial to photosynthesizing organisms. Here, we studied functions of cis-elements (AU-box and SD sequences) and a trans-acting factor (ribonuclease, RNase) in light-responsive expression in cyanobacteria. The results indicated that AU-rich nucleotides with an AU-box, UAAAUAAA, just upstream from an SD confer instability on the mRNA under darkness. An RNase E/G ...
DOI:
10.1007/s00438-007-0254-9
PubMed:
17661085

16. Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block

Author:
Gaur, Rahul; Björk, Glenn R.; Tuck, Simon; Varshney, Umesh
Source:
Journal of biosciences 2007 v.32 no.4 pp. 747-754
ISSN:
0250-5991
Subject:
Caenorhabditis elegans; Escherichia coli; anticodons; biosynthesis; cell proliferation; dietary nutrient sources; intestinal microorganisms; messenger RNA; models; neoplasms; nucleosides; phenotype; stress tolerance; sugars; transfer RNA; translation (genetics); virulence; virulent strains
Abstract:
... Queuosine (Q), a hypermodified nucleoside, occurs at the wobble position of transfer RNAs (tRNAs) with GUN anticodons. In eubacteria, absence of Q affects messenger RNA (mRNA) translation and reduces the virulence of certain pathogenic strains. In animal cells, changes in the abundance of Q have been shown to correlate with diverse phenomena including stress tolerance, cell proliferation and tumou ...
DOI:
10.1007/s12038-007-0074-4

17. Effects of Friedreich's ataxia (GAA)n·(TTC)n repeats on RNA synthesis and stability

Author:
Krasilnikova, Maria M.; Kireeva, Maria L.; Petrovic, Vladimir; Knijnikova, Nelli; Kashlev, Mikhail; Mirkin, Sergei M.
Source:
Nucleic acids research 2007 v.35 no.4 pp. 1075-1084
ISSN:
0305-1048
Subject:
messenger RNA; models; plasmids; dissociation; gene expression; transcription (genetics); neurodegenerative diseases; ataxia (disorder); DNA-directed RNA polymerase; introns; Escherichia coli
Abstract:
... Expansions of (GAA)n repeats within the first intron of the frataxin gene reduce its expression, resulting in a hereditary neurodegenerative disorder, Friedreich's ataxia. While it is generally believed that expanded (GAA)n repeats block transcription elongation, fine mechanisms responsible for gene repression are not fully understood. To follow the effects of (GAA)n·(TTC)n repeats on gene express ...
DOI:
10.1093/nar/gkl1140
PubMed:
17264130
PubMed Central:
PMC1851639

18. Efficient silencing of the gene coding for the ε subunit of DNA polymerase III in Escherichia coli is triggered by antisense RNAs featuring stability in vivo

Author:
Stefan, Alessandra; Tabler, Martin; Hochkoeppler, Alejandro
Source:
FEMS microbiology letters 2007 v.270 no.2 pp. 277-283
ISSN:
0378-1097
Subject:
DNA-directed DNA polymerase; Escherichia coli; gene silencing; genes; messenger RNA
Abstract:
... The Escherichia coli gene dnaQ coding for the ε subunit of DNA polymerase III was suppressed in vivo via antisense RNAs. To this aim, different fragments of dnaQ were cloned in reverse orientation into the pBAD-HisB vector or into pT3T7, and the corresponding antisense RNAs were conditionally expressed in vivo. Antisense transcripts featuring fast hybridization in vitro with dnaQ mRNA but lacking ...
DOI:
10.1111/j.1574-6968.2007.00679.x

19. Enhanced expression, detection and purification of recombinant proteins using RNA stem loop and tandem fusion tags

Author:
Seleem, Mohamed; Ali, Mohammed; Al-Azeem, M. W. Abd; Boyle, Stephen M.; Sriranganathan, Nammalwar
Source:
Applied microbiology and biotechnology 2007 v.75 no.6 pp. 1385-1392
ISSN:
0175-7598
Subject:
Brucella; Escherichia coli; Salmonella; detection limit; green fluorescent protein; heterologous gene expression; messenger RNA; protein synthesis; recombinant proteins
Abstract:
... The creation of a double His-tag fusion that forms a RNA stem loop in the mRNA encoding the N-terminus of the target protein is a novel approach for the enhancement of expression, purification, and detection of a recombinant protein. Compared to a single His-tag fusion, a tandem His-tag fusion RNA stem loop, located downstream of the constitutive groE and Ch promoters, enhanced heterologous gene e ...
DOI:
10.1007/s00253-007-0970-4
PubMed:
17562039

20. Escherichia coli O157:H7 gene expression in the presence of catecholamine norepinephrine

Author:
Dowd, Scot E.
Source:
FEMS microbiology letters 2007 v.273 no.2 pp. 214
ISSN:
0378-1097
Subject:
Escherichia coli O157:H7; animal pathogenic bacteria; virulence; bacterial proteins; messenger RNA; gene expression regulation; iron; gastrointestinal system; catecholamines; norepinephrine; host-pathogen relationships; pathogenesis; Escherichia coli
Abstract:
... Various forms of host stresses (e.g. physiological, psychological) are thought to influence susceptibility to pathogenic microorganisms. Catecholamines such as norepinephrine are released into the GI environment during acute stress and may influence the infective process of bacterial pathogens associated with the GI tract. To examine the effects of norepinephrine on expression of virulence factors ...
Handle:
10113/2501
DOI:
10.1111/j.1574-6968.2007.00800.x
PubMed:
17573936

21. Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites

Author:
Allemand, F.; Haentjens, J.; Chiaruttini, C.; Royer, C.; Springer, M.
Source:
Nucleic acids research 2007 v.35 no.9 pp. 3016-3031
ISSN:
0305-1048
Subject:
Escherichia coli; binding sites; gel chromatography; hybrids; messenger RNA; models; protein subunits; ribosomal RNA; ribosomal proteins; spectroscopy; translation (genetics)
Abstract:
... Ribosomal protein L20 is crucial for the assembly of the large ribosomal subunit and represses the translation of its own mRNA. L20 mRNA carries two L20-binding sites, the first folding into a pseudoknot and the second into an imperfect stem and loop. These two sites and the L20-binding site on 23S ribosomal RNA are recognized similarly using a single RNA-binding site located on one face of L20. I ...
DOI:
10.1093/nar/gkm197
PubMed:
17439971
PubMed Central:
PMC1888825

22. Fate of the sblA transcript in Streptomyces lividans and Escherichia coli

Author:
Chouayekh, Hichem; Virolle, Marie-Joëlle
Source:
FEMS microbiology letters 2007 v.276 no.1 pp. 42-47
ISSN:
0378-1097
Subject:
Escherichia coli; Streptomyces lividans; gene expression; genes; messenger RNA; nucleotides; ribonucleases; site-directed mutagenesis
Abstract:
... In Streptomyces lividans, the tight temporal regulation of the transient expression of the sblA gene was shown to involve an operator-like sequence located on the sblA transcript. This operator-like structure constitutes a stem-loop structure containing a Shine/Dalgarno-like sequence. Its destruction, by site directed mutagenesis, led to an enhancement of sblA expression. This structure thus plays ...
DOI:
10.1111/j.1574-6968.2007.00912.x
PubMed:
17877728

23. Identification of Commensal Bacterial Strains That Modulate Yersinia enterocolitica and Dextran Sodium Sulfate-Induced Inflammatory Responses: Implications for the Development of Probiotics

Author:
Frick, Julia S.; Fink, Kerstin; Kahl, Frauke; Niemiec, Maria J.; Quitadamo, Matteo; Schenk, Katrin; Autenrieth, Ingo B.
Source:
Infection and immunity 2007 v.75 no.7 pp. 3490-3497
ISSN:
0019-9567
Subject:
Bacteroides distasonis; Bacteroides vulgatus; Bifidobacterium adolescentis; Escherichia coli; Streptococcus salivarius; Yersinia enterocolitica; animal organs; bacteria; colitis; dextran; epithelial cells; gene expression; inflammation; interleukin-8; messenger RNA; mice; mucosa; pathogens; probiotics; toxicity; tumor necrosis factor-alpha; weight loss
Abstract:
... An increasing body of evidence suggests that probiotic bacteria are effective in the treatment of enteric infections, although the molecular basis of this activity remains elusive. To identify putative probiotics, we tested commensal bacteria in terms of their toxicity, invasiveness, inhibition of Yersinia-induced inflammation in vitro and in vivo, and modulation of dextran sodium sulfate (DSS)-in ...
DOI:
10.1128/IAI.00119-07
PubMed:
17485456
PubMed Central:
PMC1932957

24. Identification of the Start Codon for sphS Encoding the Phosphate-Sensing Histidine Kinase in Synechocystis sp. PCC 6803

Author:
Juntarajumnong, Waraporn; Incharoensakdi, Aran; Eaton-Rye, Julian J.
Source:
Current microbiology 2007 v.55 no.2 pp. 142-146
ISSN:
0343-8651
Subject:
Escherichia coli; Synechocystis; alkaline phosphatase; gene expression regulation; histidine kinase; messenger RNA; mutation; regulon; start codon; translation (genetics)
Abstract:
... In Synechocystis sp. PCC 6803 extracellular phosphate levels are relayed to the pho regulon via the SphS histidine kinase. In this cyanobacterium, the start codon of sphS has been assigned as a GUG, thereby predicting SphS to be a cytosolic protein lacking a putative N-terminal region found in the PhoR orthologue from Escherichia coli. Inspection upstream of sphS located an in-frame AUG positioned ...
DOI:
10.1007/s00284-007-0057-6
PubMed:
17570013

25. Improving comparability between microarray probe signals by thermodynamic intensity correction

Author:
Bruun, Georg M.; Wernersson, Rasmus; Juncker, Agnieszka S.; Willenbrock, Hanni; Nielsen, Henrik Bjørn
Source:
Nucleic acids research 2007 v.35 no.7 pp. e48
ISSN:
0305-1048
Subject:
messenger RNA; DNA; oligonucleotide probes; models; hybridization; variance; DNA microarrays; transcription (genetics); thermodynamics; yeasts; exons; introns; Escherichia coli
Abstract:
... Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between different probes. It is therefore of great interest to correct for the variation between probes. Much of thi ...
DOI:
10.1093/nar/gkl1098
PubMed:
17337437
PubMed Central:
PMC1874658

26. Inclusion of linseed and linseed expeller meal in piglet diets affects intestinal gene expression profiles

Author:
Jansman, A.J.M.; Niewold, T.A.; Hulst, M.M.
Source:
Livestock science 2007 v.108 no.1-3 pp. 23-25
ISSN:
1878-0490
Subject:
piglets; piglet feeding; feeds; linseed; linseed meal; gene expression; intestines; functional foods; Escherichia coli; animal pathogenic bacteria; bacterial infections; digestive system diseases; messenger RNA; microarray technology
DOI:
10.1016/j.livsci.2007.01.013

27. Increased production of pyruvic acid by Escherichia coli RNase G mutants in combination with cra mutations

Author:
Sakai, Taro; Nakamura, Naoko; Umitsuki, Genryou; Nagai, Kazuo; Wachi, Masaaki
Source:
Applied microbiology and biotechnology 2007 v.76 no.1 pp. 183-192
ISSN:
0175-7598
Subject:
Escherichia coli; breeding; genetic techniques and protocols; gluconeogenesis; glucose; glycolysis; isoleucine; isozymes; messenger RNA; mutants; mutation; pyruvic acid; ribonucleases; ribosomal RNA; transcription factors; valine
Abstract:
... The Escherichia coli RNase G is known as an endoribonuclease responsible for the 5′-end maturation of 16S rRNA and degradation of several specific mRNAs such as adhE and eno mRNAs. In this study, we found that an RNase G mutant derived from the MC1061 strain did not grow on a glucose minimal medium. Genetic analysis revealed that simultaneous defects of cra and ilvIH, encoding a transcriptional re ...
DOI:
10.1007/s00253-007-1006-9
PubMed:
17483940

28. Induction of Human β-Defensin 2 by the Probiotic Escherichia coli Nissle 1917 Is Mediated through Flagellin

Author:
Schlee, Miriam; Wehkamp, Jan; Altenhoefer, Artur; Oelschlaeger, Tobias A.; Stange, Eduard F.; Fellermann, Klaus
Source:
Infection and immunity 2007 v.75 no.5 pp. 2399-2407
ISSN:
0019-9567
Subject:
human cell lines; messenger RNA; humans; Salmonella Enteritidis; proteinases; bacterial adhesion; chemical analysis; cytokines; heat; antimicrobial peptides; probiotics; genes; mutants; antiserum; epithelium; flagellin; Escherichia coli
Abstract:
... Human β-defensin 2 (hBD-2) is an inducible antimicrobial peptide synthesized by the epithelium to counteract bacterial adherence and invasion. Proinflammatory cytokines, as well as certain bacterial strains, have been identified as potent endogenous inducers. Recently, we have found that hBD-2 induction by probiotic Escherichia coli Nissle 1917 was mediated through NF-κB- and AP-1-dependent pathwa ...
DOI:
10.1128/IAI.01563-06
PubMed:
17283097
PubMed Central:
PMC1865783

29. Isolation and Functional Characterization of a New Shrimp Ovarian Peritrophin with Antimicrobial Activity from Fenneropenaeus merguiensis

Author:
Loongyai, Wiriya; Avarre, Jean-Christophe; Cerutti, Martine; Lubzens, Esther; Chotigeat, Wilaiwan
Source:
Marine biotechnology 2007 v.9 no.5 pp. 624-637
ISSN:
1436-2228
Subject:
Escherichia coli; Fenneropenaeus merguiensis; Spodoptera frugiperda; Staphylococcus aureus; Vibrio harveyi; anti-infective properties; chitin; chitinase; complementary DNA; eggs; glycosylation; growth retardation; messenger RNA; minimum inhibitory concentration; pathogens; signal peptide; vitellogenesis
Abstract:
... Shrimp ovarian peritrophin (SOP), a major protein in jelly layer (JL) and cortical rods (CRs), is proposed to play a role in the protection of spawned eggs. The full sequence of SOP cDNA from Fenneropenaeus merguiensis (Fm-SOP) shares approximately 50% identity with other SOP sequences and contains several putative chitin-binding or peritrophin-A domains. Interestingly, Fm-SOP contains a putative ...
DOI:
10.1007/s10126-007-9019-z
PubMed:
17641929

30. Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach

Author:
Lang, Kathrin; Rieder, Renate; Micura, Ronald
Source:
Nucleic acids research 2007 v.35 no.16 pp. 5370-5378
ISSN:
0305-1048
Subject:
Escherichia coli; fluorescence; fluorescence emission spectroscopy; ligands; messenger RNA; models; oligonucleotides; thiamin; transcription (genetics)
Abstract:
... Riboswitches are genetic control elements within non-coding regions of mRNA. They consist of a metabolite-sensitive aptamer and an adjoining expression platform. Here, we describe ligand-induced folding of a thiamine pyrophosphate (TPP) responsive riboswitch from Escherichia coli thiM mRNA, using chemically labeled variants. Referring to a recent structure determination of the TPP/aptamer complex, ...
DOI:
10.1093/nar/gkm580
PubMed:
17693433
PubMed Central:
PMC2018614

31. Metabolic Engineering of Carotenoid Biosynthesis in Escherichia coli by Ordered Gene Assembly in Bacillus subtilis

Author:
Nishizaki, Tomoko; Tsuge, Kenji; Itaya, Mitsuhiro; Doi, Nobuhide; Yanagawa, Hiroshi
Source:
Applied and environmental microbiology 2007 v.73 no.4 pp. 1355-1361
ISSN:
0099-2240
Subject:
Bacillus subtilis; Escherichia coli; Pantoea ananatis; biochemical pathways; biosynthesis; engineering; gene expression; messenger RNA; operon; zeaxanthin
Abstract:
... We attempted to optimize the production of zeaxanthin in Escherichia coli by reordering five biosynthetic genes in the natural carotenoid cluster of Pantoea ananatis. Newly designed operons for zeaxanthin production were constructed by the ordered gene assembly in Bacillus subtilis (OGAB) method, which can assemble multiple genes in one step using an intrinsic B. subtilis plasmid transformation sy ...
DOI:
10.1128/AEM.02268-06
PubMed:
17194842
PubMed Central:
PMC1828653

32. Molecular cloning, expression, biochemical characteristics, and biomarker potential of theta class glutathione S-transferase (GST-T) from the polychaete Neanthes succinea

Author:
Rhee, J.S.; Lee, Y.M.; Hwang, D.S.; Won, E.J.; Raisuddin, S.; Shin, K.H.; Lee, J.S.
Source:
Aquatic toxicology 2007 v.83 no.2 pp. 104-115
ISSN:
0166-445X
Subject:
DNA primers; heavy metals; oxidative stress; dose response; lakes; open reading frames; biomarkers; glutathione transferase; gene expression; water temperature; Escherichia coli; water pollution; sequence analysis; messenger RNA; complementary DNA; copper; Polychaeta; pollutants; enzyme inhibitors; molecular cloning; antioxidants; reverse transcriptase polymerase chain reaction; metallothionein; pH; kinetics; environmental indicators; South Korea
Abstract:
... We cloned and sequenced the full-length cDNA of a theta class glutathione S-transferase (GST-T) from the polychaete Neanthes succinea. The open reading frame of N. succinea GST-T cDNA was 678 bp and encoded 226 amino acid residues. We generated recombinant N. succinea GST-T by expression in transformed Escherichia coli and studied the kinetic properties as well as the effects of inhibitors, pH, an ...
DOI:
10.1016/j.aquatox.2007.03.015

33. Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations

Author:
Ishii, Nobuyoshi; Nakahigashi, Kenji; Baba, Tomoya; Robert, Martin; Soga, Tomoyoshi; Kanai, Akio; Hirasawa, Takashi; Naba, Miki; Hirai, Kenta; Hoque, Aminul; Ho, Pei Yee; Kakazu, Yuji; Sugawara, Kaori; Igarashi, Saori; Harada, Satoshi; Masuda, Takeshi; Sugiyama, Naoyuki; Togashi, Takashi; Hasegawa, Miki; Takai, Yuki; Yugi, Katsuyuki; Arakawa, Kazuharu; Iwata, Nayuta; Toya, Yoshihiro; Nakayama, Yoichi; Nishioka, Takaaki; Shimizu, Kazuyuki; Mori, Hirotada; Tomita, Masaru
Source:
Science 2007 v.316 no.5824 pp. 593-597
ISSN:
0036-8075
Subject:
Escherichia coli; genes; messenger RNA; metabolites; proteins
Abstract:
... Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Over ...
DOI:
10.1126/science.1132067

34. Polyadenylation of a functional mRNA controls gene expression in Escherichia coli

Author:
Joanny, Géraldine; Derout, Jacques Le; Bréchemier-Baey, Dominique; Labas, Valérie; Vinh, Joelle; Régnier, Philippe; Hajnsdorf, Eliane
Source:
Nucleic acids research 2007 v.35 no.8 pp. 2494-2502
ISSN:
0305-1048
Subject:
Escherichia coli; bacteria; chemical elements; eukaryotic cells; gene expression; genes; messenger RNA; quality control; ribonucleases
Abstract:
... Although usually implicated in the stabilization of mRNAs in eukaryotes, polyadenylation was initially shown to destabilize RNA in bacteria. All the data are consistent with polyadenylation being part of a quality control process targeting folded RNA fragments and non-functional RNA molecules to degradation. We report here an example in Escherichia coli, where polyadenylation directly controls the ...
DOI:
10.1093/nar/gkm120
PubMed:
17395638
PubMed Central:
PMC1885654

35. Proinflammatory cytokine mRNA expression in mammary tissue of sows following intramammary inoculation with Escherichia coli

Author:
Zhu, Y.; Berg, M.; Fossum, C.; Magnusson, U.
Source:
Veterinary immunology and immunopathology 2007 v.116 no.1-2 pp. 98-103
ISSN:
0165-2427
Subject:
correlation; mastitis; protein synthesis; tumor necrosis factors; messenger RNA; interleukins; swine diseases; sows; parturition; mammary glands; inflammation; gene expression; immune response; immune system; Escherichia infections; signs and symptoms (animals and humans); Escherichia coli
Abstract:
... The expression of the proinflammatory cytokines interleukin-1β (IL-1β), IL-6, IL-8, and tumor necrosis factor-α (TNF-α) mRNAs was determined by reverse transcription-PCR (RT-PCR) analysis of biopsies from the mammary glands of sows. The biopsies were collected before and 24 h after intramammary inoculation of 12 pregnant sows with Escherichia coli (E. coli). Four of the sows developed clinical sig ...
DOI:
10.1016/j.vetimm.2006.12.003

36. Relationship Between mRNA Stability and Length: An Old Question with a New Twist

Author:
Feng, Liang; Niu, Deng-Ke
Source:
Biochemical genetics 2007 v.45 no.1-2 pp. 131-137
ISSN:
0006-2928
Subject:
Bacillus subtilis; Escherichia coli; Saccharomyces cerevisiae; gene expression; half life; mechanical damage; messenger RNA
Abstract:
... The half-life of individual mRNA plays a central role in controlling the level of gene expression. However, the determinants of mRNA stability have not yet been well defined. Most previous studies suggest that mRNA length does not affect its stability. Here, we show significant negative correlations between mRNA length and stability in human and Escherichia coli, but not in Saccharomyces cerevisia ...
DOI:
10.1007/s10528-006-9059-5

37. Release Factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies

Author:
Zoldák, Gabriel; Redecke, Lars; Svergun, Dmitri I.; Konarev, Peter V.; Voertler, C. Stefan; Dobbek, Holger; Sedlák, Erik; Sprinzl, Mathias
Source:
Nucleic acids research 2007 v.35 no.4 pp. 1343-1353
ISSN:
0305-1048
Subject:
Escherichia coli; Thermus thermophilus; X-radiation; calorimetry; circular dichroism spectroscopy; crystal structure; melting; messenger RNA; physiological state; protein synthesis; ribosomes; stop codon; temperature; thermodynamics
Abstract:
... Prokaryotic class I release factors (RFs) respond to mRNA stop codons and terminate protein synthesis. They interact with the ribosomal decoding site and the peptidyl-transferase centre bridging these 75 Å distant ribosomal centres. For this an elongated RF conformation, with partially unfolded core domains II·III·IV is required, which contrasts the known compact RF crystal structures. The crystal ...
DOI:
10.1093/nar/gkl696
PubMed:
17272297
PubMed Central:
PMC1849895

38. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism

Author:
Choonee, Nasslie; Even, Sergine; Zig, Lena; Putzer, Harald
Source:
Nucleic acids research 2007 v.35 no.5 pp. 1578-1588
ISSN:
0305-1048
Subject:
Bacillus subtilis; Escherichia coli; biosynthesis; messenger RNA; models; molecular mimicry; operon; phylogeny; protein synthesis; regulatory sequences; ribosomal RNA; ribosomal proteins; transcription (genetics); translation (genetics)
Abstract:
... In contrast to Escherichia coli no molecular mechanism controlling the biosynthesis of ribosomal proteins has been elucidated in Gram-positive organisms. Here we show that the expression of the Bacillus subtilis infC-rpmI-rplT operon encoding translation factor IF3 and the ribosomal proteins L35 and L20 is autoregulated by a complex transcription attenuation mechanism. It implicates a 200-bp leade ...
DOI:
10.1093/nar/gkm011
PubMed:
17289755
PubMed Central:
PMC1865079

39. RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition

Author:
Ameres, Stefan L.; Shcherbakov, Dmitry; Nikonova, Ekaterina; Piendl, Wolfgang; Schroeder, Renée; Semrad, Katharina
Source:
Nucleic acids research 2007 v.35 no.11 pp. 3752-3763
ISSN:
0305-1048
Subject:
Escherichia coli; Methanococcus; RNA conformation; bacteria; bacteriophages; catalytic activity; introns; messenger RNA; mutational analysis; phylogeny; protein subunits; ribosomal RNA; ribosomal proteins; ribosomes; thymidylate synthase
Abstract:
... RNA chaperone activity is defined as the ability of proteins to either prevent RNA from misfolding or to open up misfolded RNA conformations. One-third of all large ribosomal subunit proteins from E. coli display this activity, with L1 exhibiting one of the highest activities. Here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the RNA chaperone activity of L1 is conse ...
DOI:
10.1093/nar/gkm318
PubMed:
17517772
PubMed Central:
PMC1920258

40. RNase E Is Required for Induction of the Glutamate-Dependent Acid Resistance System in Escherichia coli

Author:
TAKADA, Ayako; UMITSUKI, Genryou; NAGAI, Kazuo; WACHI, Masaaki
Source:
Bioscience, biotechnology, and biochemistry 2007 v.71 no.1 pp. 158-164
ISSN:
1347-6947
Subject:
Escherichia coli; RNA-binding proteins; acid tolerance; amino acids; glutamate decarboxylase; isozymes; messenger RNA; mutants; pH; ribonucleases; ribosomal RNA; temperature; transfer RNA
Abstract:
... The Escherichia coli RNase E is an essential endoribonuclease involved in processing and/or degradation of rRNAs, tRNAs, and non-coding small RNAs as well as many mRNAs. It is known that RNase E activity is somehow regulated by an RNA-binding protein Hfq, at least in some cases. We searched for proteins that showed changes in expression in both hfq::cat and rne-1 mutant cells as compared with the ...
DOI:
10.1271/bbb.60423

41. Sigma E controls biogenesis of the antisense RNA MicA

Author:
Udekwu, Klas I.; Wagner, E. Gerhart H.
Source:
Nucleic acids research 2007 v.35 no.4 pp. 1279-1288
ISSN:
0305-1048
Subject:
Escherichia coli; Gram-negative bacteria; antisense RNA; biogenesis; ethanol; gene expression regulation; gene overexpression; heat stress; messenger RNA; mutants; outer membrane proteins; regulon; stress response; transcription (genetics); translation (genetics)
Abstract:
... Adaptation stress responses in the Gram-negative bacterium Escherichia coli and its relatives involve a growing list of small regulatory RNAs (sRNAs). Previous work by us and others showed that the antisense RNA MicA downregulates the synthesis of the outer membrane protein OmpA upon entry into stationary phase. This regulation is Hfq-dependent and occurs by MicA-dependent translational inhibition ...
DOI:
10.1093/nar/gkl1154
PubMed:
17267407
PubMed Central:
PMC1851643

42. Surface Expression of Toll-Like Receptor 9 Is Upregulated on Intestinal Epithelial Cells in Response to Pathogenic Bacterial DNA

Author:
Ewaschuk, Julia B.; Backer, Jody L.; Churchill, Thomas A.; Obermeier, Florian; Krause, Denis O.; Madsen, Karen L.
Source:
Infection and immunity 2007 v.75 no.5 pp. 2572-2579
ISSN:
0019-9567
Subject:
secretion; epithelial cells; intestinal mucosa; Salmonella Dublin; Bifidobacterium breve; DNA; enzyme-linked immunosorbent assay; gene expression; chloroquine; gene expression regulation; pathogens; interleukin-8; Escherichia coli; messenger RNA; serotypes; mice; fluorescent antibody technique; virulent strains; inflammation; flow cytometry; microorganisms; reverse transcriptase polymerase chain reaction
Abstract:
... Colonic epithelial cells are constantly exposed to high levels of bacterial DNA in the intestinal lumen and must recognize and respond appropriately to pathogens, while they maintain a tolerance to nonpathogenic commensal bacterial strains. Bacterial DNA is recognized by Toll-like receptor 9 (TLR9). The aim of this study was to investigate TLR9 expression and localization in colonic epithelial cel ...
DOI:
10.1128/IAI.01662-06
PubMed:
17325049
PubMed Central:
PMC1865769

43. Thermus thermophilus L4 ribosomal protein: purification and sensitivity alteration against erythromycin of E. coli cells harboring a single amino acid mutant of TthL4 within its extended loop

Author:
Leontiadou, F.; Tsagkalia, A.; Choli-Papadopoulou, T.
Source:
Amino acids 2007 v.33 no.3 pp. 463-468
ISSN:
0939-4451
Subject:
Escherichia coli; Thermotoga maritima; Thermus thermophilus; alanine; drug resistance; drugs; erythromycin; glutamic acid; ion exchange chromatography; messenger RNA; mutants; mutation; ribosomal RNA; ribosomes; thermophilic bacteria
Abstract:
... Protein L4 from the thermophilic bacterium Thermus thermophilus (TthL4) was heterologously overproduced in Escherichia coli cells and purified under native conditions by using ion exchange chromatography. Although it's known strong binding to RNA (23S rRNA as well as mRNA) the yield of the purified protein was 6 mg per 10 g of cells and it is similar to that referred for Thermotoga maritima L4 rib ...
DOI:
10.1007/s00726-006-0438-3
PubMed:
17048124

44. The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli

Author:
Chatterji, Dipankar; Ogawa, Yoshito; Shimada, Tomohiro; Ishihama, Akira
Source:
FEMS microbiology letters 2007 v.267 no.1 pp. 51-55
ISSN:
0378-1097
Subject:
messenger RNA; starvation; stress response; DNA microarrays; gene expression; ribosomal proteins; operon; DNA-directed RNA polymerase; Escherichia coli
Abstract:
... The rpoZ gene for the omega subunit of Escherichia coli RNA polymerase constitutes single operon with the spoT gene, which is responsible for the maintenance of stringent response under nutrient starvation conditions. To identify the physiological role of the omega subunit, we compared the gene expression profile of wild-type Escherichia coli with that of an rpoZ deleted strain by microarray analy ...
DOI:
10.1111/j.1574-6968.2006.00532.x

45. Translational control and target recognition by Escherichia coli small RNAs in vivo

Author:
Urban, Johannes H.; Vogel, Jörg
Source:
Nucleic acids research 2007 v.35 no.3 pp. 1018-1037
ISSN:
0305-1048
Subject:
Escherichia coli; Vibrio; bacteria; gene expression; green fluorescent protein; messenger RNA; mutants; non-coding RNA; ribonucleases; translation (genetics)
Abstract:
... Small non-coding RNAs (sRNAs) are an emerging class of regulators of bacterial gene expression. Most of the regulatory Escherichia coli sRNAs known to date modulate translation of trans-encoded target mRNAs. We studied the specificity of sRNA target interactions using gene fusions to green fluorescent protein (GFP) as a novel reporter of translational control by bacterial sRNAs in vivo. Target seq ...
DOI:
10.1093/nar/gkl1040
PubMed:
17264113
PubMed Central:
PMC1807950

46. Up-regulation of yggG promotes the survival of Escherichia coli cells containing Era-1 mutant protein

Author:
Huang, Yong; Zhang, Bin; Dong, Ke; Zhang, XiaoNan; Hou, LiChao; Wang, Tao; Chen, NanChun; Chen, SuMin
Source:
FEMS microbiology letters 2007 v.275 no.1 pp. 8-15
ISSN:
0378-1097
Subject:
DNA; Escherichia coli; amino acid sequences; bacteriophages; gene expression; gene expression regulation; genes; guanosinetriphosphatase; heat; heat shock proteins; messenger RNA; metalloproteinases; microbial growth; mutants; stress response
Abstract:
... Era is a highly conserved GTPase essential for bacterial growth. Using a digoxigenin-labeled Era protein to screen a phage expression library of Escherichia coli genomic DNA, yggG, a gene that encodes a putative zinc metalloprotease was isolated and characterized. The deduced amino acid sequence of YggG showed high degrees of similarity to some reported heat shock proteins. In this study, the dire ...
DOI:
10.1111/j.1574-6968.2007.00860.x
PubMed:
17651431

47. Using DNA sequencing electrophoresis compression artifacts as reporters of stable mRNA structures affecting gene expression

Author:
Kapoor, Divya; Chandrayan, Sanjeev Kumar; Ahmed, Shubbir; Guptasarma, Purnananda
Source:
Electrophoresis 2007 v.28 no.21 pp. 3862-3867
ISSN:
0173-0835
Subject:
DNA; Escherichia coli; Rhodothermus marinus; electrophoresis; gene overexpression; genes; messenger RNA; mutation; nucleotide sequences; oligonucleotides; ribosomes; sequence analysis; translation (genetics)
Abstract:
... The formation of secondary structure in oligonucleotide DNA is known to lead to "compression" artifacts in electropherograms produced through DNA sequencing. Separately, the formation of secondary structure in mRNA is known to suppress translation; in particular, when such structures form in a region covered by the ribosome either during, or shortly after, initiation of translation. Here, we demon ...
DOI:
10.1002/elps.200700359